view usearch_map_reads_to_otu/scripts/otu_table_transform.py @ 0:c10d09023766 draft

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import sys, os
#sys.path.insert(0, 'scripts');
import parseFasta

# Create OTU Table
# OTU_Lable | Count | Sequence
# 
# Author: Anne Kunert
#

OTUmap = sys.argv[1]
OTUcount = sys.argv[2]

def transform(file):
  seq = parseFasta.FastaParser(OTUmap)
  with open(file) as f:
    lis=[x.split() for x in f]
  end=""
  line=""
  myseq=""
  for x in zip(*lis):
    otu_lable = x[0]
    for item in seq:
      if item == otu_lable:
        myseq = seq.records[item]['sequence']
        myseq = myseq.replace('\n','')
    for y in x:
      line= line+str(y)+"\t"
    print(line+"\t"+myseq)
    line=""
    myseq=""
#
transform(OTUcount)